Resource
| Id | ATAC-seq/ENCSR163KRG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR163KRG [biosample_summary="Homo sapiens HG03469"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN220NNS|/analyses/ENCAN220NNS/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF430HQS|/files/ENCFF430HQS/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.820312. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF430HQS|/files/ENCFF430HQS/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. audit_warning: According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have either >150k reproducible peaks in an overlap peaks file, or >70k in an IDR thresholded peaks file. 100-150k or 50-70k peaks respectively is acceptable, and <100k or <50k respectively is not compliant. File(s) {ENCFF187ZKG|/files/ENCFF187ZKG/} (overlap peaks) and {ENCFF505YPT|/files/ENCFF505YPT/} (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 131170 and 67312 peaks. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR163KRG | float |
ATAC-seq_ENCSR163KRG |
ATAC-seq ENCSR163KRG [biosample_summary="Homo sapiens HG03469"]
|
 |
[1.68, 39.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 43646811 | 1.36% | 97359 |
| chr1 | 3828808 | 1.54% | 8433 |
| chr2 | 3873807 | 1.60% | 8850 |
| chr3 | 3178343 | 1.60% | 7282 |
| chr4 | 2668866 | 1.40% | 6153 |
| chr5 | 2745478 | 1.51% | 6275 |
| chr6 | 2968178 | 1.74% | 6677 |
| chr7 | 2494935 | 1.57% | 5642 |
| chr8 | 2278036 | 1.57% | 5212 |
| chr9 | 1713094 | 1.24% | 3806 |
| chr10 | 2095877 | 1.57% | 4708 |
| chr11 | 2045536 | 1.51% | 4579 |
| chr12 | 2167858 | 1.63% | 4820 |
| chr13 | 1276945 | 1.12% | 2889 |
| chr14 | 1308919 | 1.22% | 2820 |
| chr15 | 1179119 | 1.16% | 2575 |
| chr16 | 1150776 | 1.27% | 2350 |
| chr17 | 1312069 | 1.58% | 2698 |
| chr18 | 1070296 | 1.33% | 2475 |
| chr19 | 1076726 | 1.84% | 1980 |
| chr20 | 895175 | 1.39% | 1990 |
| chr21 | 438060 | 0.94% | 935 |
| chr22 | 476461 | 0.94% | 949 |
| chrX | 1287955 | 0.83% | 2971 |
| chrY | 115494 | 0.20% | 290 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 97359 | 150 | 2368 | 448.31 | 376 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF187ZKG.bed.gz | 3.15 MB | 7b91995f196b3e40880860915c318cfb |
| ENCFF187ZKG.tabix.bed.gz | 1.04 MB | 562265f8a0624493c03451efd776dce3 |
| ENCFF187ZKG.tabix.bed.gz.tbi | 444.63 KB | c32b1c83140689fa644d7e3013e1f860 |
| genomic_resource.yaml | 3.05 KB | 642ccd2158272c30384097c0a4df22e6 |
| statistics/ |